Pub Date : 2010-03-19DOI: 10.2174/18741967010030100032
G. Eckert
Lipid rafts are specialized plasma membrane micro-domains highly enriched in cholesterol, sphingolipids and glycosylphosphatidylinositol (GPI) anchored proteins. Lipid rafts are thought to be located in the exofacial leaflet of plasma membranes. Functionally, lipid rafts are involved in intracellular trafficking of proteins and lipids, secretory and endocytotic pathways, signal transduction, inflammation and in cell-surface proteolysis. There has been substantial interest in lipid rafts in brain, both with respect to normal functioning and with certain neurodegenerative diseases. Based on the impact of lipid rafts on multitude biochemical pathways, modulation of lipid rafts is used to study related disease pathways and probably offers a target for pharmacological intervention. Lipid rafts can be targeted by modulation of its main components, namely cholesterol and sphingolipids. Other approaches include the modulation of membrane dynamics and it has been reported that protein-lipid interactions can vary the occurrence and composition of these membrane micro-domains. The present review summarizes the possibilities to modulate lipid rafts with focus on neuronal cells.
{"title":"Manipulation of Lipid Rafts in Neuronal Cells","authors":"G. Eckert","doi":"10.2174/18741967010030100032","DOIUrl":"https://doi.org/10.2174/18741967010030100032","url":null,"abstract":"Lipid rafts are specialized plasma membrane micro-domains highly enriched in cholesterol, sphingolipids and glycosylphosphatidylinositol (GPI) anchored proteins. Lipid rafts are thought to be located in the exofacial leaflet of plasma membranes. Functionally, lipid rafts are involved in intracellular trafficking of proteins and lipids, secretory and endocytotic pathways, signal transduction, inflammation and in cell-surface proteolysis. There has been substantial interest in lipid rafts in brain, both with respect to normal functioning and with certain neurodegenerative diseases. Based on the impact of lipid rafts on multitude biochemical pathways, modulation of lipid rafts is used to study related disease pathways and probably offers a target for pharmacological intervention. Lipid rafts can be targeted by modulation of its main components, namely cholesterol and sphingolipids. Other approaches include the modulation of membrane dynamics and it has been reported that protein-lipid interactions can vary the occurrence and composition of these membrane micro-domains. The present review summarizes the possibilities to modulate lipid rafts with focus on neuronal cells.","PeriodicalId":22949,"journal":{"name":"The Open Biology Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79449445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-01-13DOI: 10.2174/18741967010030100001
M. Songpim, P. Vaithanomsat, S. Chuntranuluck
The parameters affecting the production of pectate lyase from P. polymyxa N10 were studied using the response surface methodology agitation rate (X1, 100-300 rpm), temperature (X2, 25-45 o C) and pH (X3, 5.5-9.5). The most significant factors influencing enzyme production were temperature and pH. The second order polynomial regression model obtained was fitted and found adequate, with an R 2 of 0.9600 (p < 0.001). A maximum pectate lyase activity of 84.5 U/ml was attained in 72 h of cultivation at agitation rate 200 rpm, temperature 35 o C and pH 8. Optimizations of agitation rate and aeration on pectate lyase production were also carried out in a 5-l stirred-tank bioreactor. The aeration rate was varied in the range of 0.5-2 vvm at agitation rate of 200 rpm (temperature 35 o C and initial pH 8). At agitation rate of 200 rpm, the shear force was high and then decreased the pectate lyase activity due to its negative effect on the enzyme structure. A maximum pectate lyase activity of 110.42 U/ml in the bioreactor was close to that obtained from the shake flask fermentation study.
{"title":"Optimization of Pectate Lyase Production from Paenibacillus polymyxa N10 using Response Surface Methodology","authors":"M. Songpim, P. Vaithanomsat, S. Chuntranuluck","doi":"10.2174/18741967010030100001","DOIUrl":"https://doi.org/10.2174/18741967010030100001","url":null,"abstract":"The parameters affecting the production of pectate lyase from P. polymyxa N10 were studied using the response surface methodology agitation rate (X1, 100-300 rpm), temperature (X2, 25-45 o C) and pH (X3, 5.5-9.5). The most significant factors influencing enzyme production were temperature and pH. The second order polynomial regression model obtained was fitted and found adequate, with an R 2 of 0.9600 (p < 0.001). A maximum pectate lyase activity of 84.5 U/ml was attained in 72 h of cultivation at agitation rate 200 rpm, temperature 35 o C and pH 8. Optimizations of agitation rate and aeration on pectate lyase production were also carried out in a 5-l stirred-tank bioreactor. The aeration rate was varied in the range of 0.5-2 vvm at agitation rate of 200 rpm (temperature 35 o C and initial pH 8). At agitation rate of 200 rpm, the shear force was high and then decreased the pectate lyase activity due to its negative effect on the enzyme structure. A maximum pectate lyase activity of 110.42 U/ml in the bioreactor was close to that obtained from the shake flask fermentation study.","PeriodicalId":22949,"journal":{"name":"The Open Biology Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76507769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-01-04DOI: 10.2174/1874196700902020176
J. Reumers, F. Rousseau, J. Schymkowitz
{"title":"Multiple Evolutionary Mechanisms Reduce Protein Aggregation~!2009-04-21~!2009-07-09~!2010-01-02~!","authors":"J. Reumers, F. Rousseau, J. Schymkowitz","doi":"10.2174/1874196700902020176","DOIUrl":"https://doi.org/10.2174/1874196700902020176","url":null,"abstract":"","PeriodicalId":22949,"journal":{"name":"The Open Biology Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79389258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-01-04DOI: 10.2174/1874196700902020200
L. Cassina, G. Casari
Mitochondria are eukaryotic intracellular organelles that still bear the signatures of their prokaryotic ancestor and require nuclear assistance. They generously dispense energy to cells, but are also involved in several biosynthetic processes, as well as in cell signalling pathways and programmed cell death. Mitochondria are partitioned into four intra-organelle compartments: the outer membrane, the inner membrane, the intermembrane space and the matrix. Each compartment contains a unique set of proteins and a personalised system for guaranteeing protein homeostasis. What follows is a survey of the function and topology of the multiple systems that operate the concerted action of protein sorting and folding in the four mitochondrial compartments.
{"title":"The Tightly Regulated and Compartmentalised Import, Sorting and Folding of Mitochondrial Proteins~!2009-05-06~!2009-08-12~!2010-01-02~!","authors":"L. Cassina, G. Casari","doi":"10.2174/1874196700902020200","DOIUrl":"https://doi.org/10.2174/1874196700902020200","url":null,"abstract":"Mitochondria are eukaryotic intracellular organelles that still bear the signatures of their prokaryotic ancestor and require nuclear assistance. They generously dispense energy to cells, but are also involved in several biosynthetic processes, as well as in cell signalling pathways and programmed cell death. Mitochondria are partitioned into four intra-organelle compartments: the outer membrane, the inner membrane, the intermembrane space and the matrix. Each compartment contains a unique set of proteins and a personalised system for guaranteeing protein homeostasis. What follows is a survey of the function and topology of the multiple systems that operate the concerted action of protein sorting and folding in the four mitochondrial compartments.","PeriodicalId":22949,"journal":{"name":"The Open Biology Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80915202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-01-04DOI: 10.2174/1874196700902020193
A. Mikecz
The nucleus represents a cellular control unit that regulates all events concerning the storage and processing of DNA and RNA. It is organized by highly crowded, dynamic assemblies of proteins and nucleic acids in molecular machines, ribonucleoprotein complexes, clusters of ongoing nuclear processes, nuclear bodies, and chromatin. This review discusses the occurrence of nuclear protein aggregation with special emphasis on the functional architecture of the nucleus, and quality control by the ubiquitin-proteasome system.
{"title":"Protein Aggregation in the Cell Nucleus: Structure, Function and Topology~!2009-04-10~!2009-06-05~!2010-01-02~!","authors":"A. Mikecz","doi":"10.2174/1874196700902020193","DOIUrl":"https://doi.org/10.2174/1874196700902020193","url":null,"abstract":"The nucleus represents a cellular control unit that regulates all events concerning the storage and processing of DNA and RNA. It is organized by highly crowded, dynamic assemblies of proteins and nucleic acids in molecular machines, ribonucleoprotein complexes, clusters of ongoing nuclear processes, nuclear bodies, and chromatin. This review discusses the occurrence of nuclear protein aggregation with special emphasis on the functional architecture of the nucleus, and quality control by the ubiquitin-proteasome system.","PeriodicalId":22949,"journal":{"name":"The Open Biology Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78219600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-01-04DOI: 10.2174/1874196700902020161
M. Stefani
The theme of protein folding is increasingly becoming a hot topic for the attention of not only biochemists, biophysicists, biotechnologists, cell and molecular biologists but also of researchers in the fields of molecular evolution and molecular medicine. Actually, protein folding has progressively revealed multi-faceted aspects linking it to two other, strictly related aspects, protein misfolding and aggregation that are being shown to be at the basis of many physiological and pathological processes. In the past 15-20 years, all these themes have undergone profound changes of paradigms. The energy landscape theory of protein folding has provided a solid theoretical basis to interpret old experimental data and to design new experimental approaches also taking benefit of newly introduced spectroscopic and fluorescence methods. It has also exploited the single-mutant approach first introduced by Alan Fesht to assess the contribution of each single residue in the overall folding process. Presently, we can consider with confidence the possibility that in a near future we will be able to decrypt the folding code encrypted in the amino acid sequence of each polypeptide chain enabling us to propose with good approximation a three-dimensional structure from any given one-dimensional string of amino acid residues under specific environmental conditions. Protein misfolding is increasingly seen as much more than a mere defect of protein folding. Rather, presently it is considered the other side of the coin of protein folding. The protein conformational states available to a polypeptide chain go well beyond the natively folded, biologically active, form. Aberrantly folded, or misfolded, states in dynamic equilibrium with the correctly folded conformation appear continuously in the population of a protein's molecules. Accordingly, a protein solution can be considered a collection of different conformational states undergoing very rapid interchange where the native state is the most highly populated, which occupies a minimal energy state. This is the theoretical basis to understand the effects of structural (amino acid substitutions) or environmental (pH, temperature, chemical modification, presence of surfaces or stabilising ligands, protein over-expression) perturbations affecting the folded-misfolded equilibrium with the resulting quantitative modification of the different structures of the polypeptide chain populated at the equilibrium. The review by Paavo Kinnunen strengthens the importance of surfaces in affecting the behaviour of polypeptide chains making them more or less susceptible to misfolding/unfolding. This is a very important point, considering that the intracellular milieu is dramatically crowded by macromolecules and membranes and hence of surfaces with different …
{"title":"Editorial: Special Issue on Protein Folding and Aggregation","authors":"M. Stefani","doi":"10.2174/1874196700902020161","DOIUrl":"https://doi.org/10.2174/1874196700902020161","url":null,"abstract":"The theme of protein folding is increasingly becoming a hot topic for the attention of not only biochemists, biophysicists, biotechnologists, cell and molecular biologists but also of researchers in the fields of molecular evolution and molecular medicine. Actually, protein folding has progressively revealed multi-faceted aspects linking it to two other, strictly related aspects, protein misfolding and aggregation that are being shown to be at the basis of many physiological and pathological processes. In the past 15-20 years, all these themes have undergone profound changes of paradigms. The energy landscape theory of protein folding has provided a solid theoretical basis to interpret old experimental data and to design new experimental approaches also taking benefit of newly introduced spectroscopic and fluorescence methods. It has also exploited the single-mutant approach first introduced by Alan Fesht to assess the contribution of each single residue in the overall folding process. Presently, we can consider with confidence the possibility that in a near future we will be able to decrypt the folding code encrypted in the amino acid sequence of each polypeptide chain enabling us to propose with good approximation a three-dimensional structure from any given one-dimensional string of amino acid residues under specific environmental conditions. Protein misfolding is increasingly seen as much more than a mere defect of protein folding. Rather, presently it is considered the other side of the coin of protein folding. The protein conformational states available to a polypeptide chain go well beyond the natively folded, biologically active, form. Aberrantly folded, or misfolded, states in dynamic equilibrium with the correctly folded conformation appear continuously in the population of a protein's molecules. Accordingly, a protein solution can be considered a collection of different conformational states undergoing very rapid interchange where the native state is the most highly populated, which occupies a minimal energy state. This is the theoretical basis to understand the effects of structural (amino acid substitutions) or environmental (pH, temperature, chemical modification, presence of surfaces or stabilising ligands, protein over-expression) perturbations affecting the folded-misfolded equilibrium with the resulting quantitative modification of the different structures of the polypeptide chain populated at the equilibrium. The review by Paavo Kinnunen strengthens the importance of surfaces in affecting the behaviour of polypeptide chains making them more or less susceptible to misfolding/unfolding. This is a very important point, considering that the intracellular milieu is dramatically crowded by macromolecules and membranes and hence of surfaces with different …","PeriodicalId":22949,"journal":{"name":"The Open Biology Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73350648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-01-04DOI: 10.2174/1874196700902020228
V. Bellotti, M. Stoppini
{"title":"Protein Misfolding Diseases~!2009-04-27~!2009-06-22~!2010-01-02~!","authors":"V. Bellotti, M. Stoppini","doi":"10.2174/1874196700902020228","DOIUrl":"https://doi.org/10.2174/1874196700902020228","url":null,"abstract":"","PeriodicalId":22949,"journal":{"name":"The Open Biology Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82197074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-01-04DOI: 10.2174/1874196700902020185
K. Marshall, L. Serpell
{"title":"Insights into the Structure of Amyloid Fibrils~!2009-04-21~!2009-07-09~!2010-01-02~!","authors":"K. Marshall, L. Serpell","doi":"10.2174/1874196700902020185","DOIUrl":"https://doi.org/10.2174/1874196700902020185","url":null,"abstract":"","PeriodicalId":22949,"journal":{"name":"The Open Biology Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78549645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-01-04DOI: 10.2174/1874196700902020222
C. Glabe
{"title":"Amyloid Oligomer Structures and Toxicity~!2009-04-30~!2009-07-07~!2010-01-02~!","authors":"C. Glabe","doi":"10.2174/1874196700902020222","DOIUrl":"https://doi.org/10.2174/1874196700902020222","url":null,"abstract":"","PeriodicalId":22949,"journal":{"name":"The Open Biology Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80823903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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